If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ), 'gf_id' => 'HOM05D001053', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001053' ), 'data_identifier' => 'HOM05D001053', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001053', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '576', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04800' => 'bna', 'A02p41350' => 'bna', 'A02p41380' => 'bna', 'A03p40690' => 'bna', 'A03p46750' => 'bna', 'A05p31110' => 'bna', 'A09p07210' => 'bna', 'A09p65890' => 'bna', 'Aa31LG11G2250' => 'aar', 'Aa31LG8G5390' => 'aar', 'Aa31sc139G30' => 'aar', 'Aa31sc146G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2555' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4175' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1571' => 'aag', 'Actinidia04826' => 'ach', 'Actinidia04827' => 'ach', 'Actinidia06612' => 'ach', 'Actinidia16123' => 'ach', 'Actinidia31025' => 'ach', 'Actinidia35480' => 'ach', 'Ah.02g121650' => 'amhyb', 'Ah.02g121660' => 'amhyb', 'Ah.11g047830' => 'amhyb', 'Ah.15g100110' => 'amhyb', 'Ah.15g100120' => 'amhyb', 'AL1G18880' => 'aly', 'AL299U10010' => 'aly', 'AL3G31840' => 'aly', 'AL7G18080' => 'aly', 'AL8G37710' => 'aly', 'AL8G37720' => 'aly', 'Aqoxy1G00657' => 'aox', 'Aqoxy208s002' => 'aox', 'Aqoxy3G00397' => 'aox', 'Aqoxy3G03637' => 'aox', 'Aqoxy4G01666' => 'aox', 'Aqoxy5G02258' => 'aox', 'arahy.Tifrunner.gnm1.ann1.30WRMH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJM2KG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EY28RQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JNKP0R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MVN91E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7KHNQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XDJV4T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YD5ENU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YLDT1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z2UDZG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD7DCY' => 'arhy', 'AT1G08460' => 'ath', 'AT3G18520' => 'ath', 'AT4G09784' => 'ath', 'AT4G33470' => 'ath', 'AT5G61050' => 'ath', 'AT5G61060' => 'ath', 'AT5G61070' => 'ath', 'ATR0064G039' => 'atr', 'ATR0115G004' => 'atr', 'ATR0709G070' => 'atr', 'ATR0772G212' => 'atr', 'Atru.chr3.3124' => 'acertr', 'Atru.chr4.2605' => 'acertr', 'Atru.chr4.2606' => 'acertr', 'Atru.chr4.871' => 'acertr', 'Atru.chr9.430' => 'acertr', 'AUR62001548' => 'cqu', 'AUR62003584' => 'cqu', 'AUR62008521' => 'cqu', 'AUR62017897' => 'cqu', 'AUR62020235' => 'cqu', 'AUR62021568' => 'cqu', 'AUR62021569' => 'cqu', 'AUR62032194' => 'cqu', 'AUR62036959' => 'cqu', 'BcaB04g20773' => 'bca', 'BcaB06g25897' => 'bca', 'BcaB07g34221' => 'bca', 'BcaB07g34222' => 'bca', 'BcaC01g03696' => 'bca', 'BcaC03g18073' => 'bca', 'BcaC04g23464' => 'bca', 'BcaC04g23465' => 'bca', 'BcaC05g28608' => 'bca', 'BcaC06g33180' => 'bca', 'BcaC07g41944' => 'bca', 'BcaC09g48809' => 'bca', 'BcaC09g52163' => 'bca', 'BolC1t04531H' => 'bol', 'BolC2t12181H' => 'bol', 'BolC3t17246H' => 'bol', 'BolC5t33436H' => 'bol', 'BolC5t33437H' => 'bol', 'BolC7t45003H' => 'bol', 'BolC8t52529H' => 'bol', 'BolC9t53719H' => 'bol', 'BolC9t53720H' => 'bol', 'BraA01t00463Z' => 'bra', 'BraA01t03669Z' => 'bra', 'BraA02t09080Z' => 'bra', 'BraA03t13225Z' => 'bra', 'BraA03t13226Z' => 'bra', 'BraA03t13797Z' => 'bra', 'BraA05t21952Z' => 'bra', 'BraA09t36370Z' => 'bra', 'BraA09t36371Z' => 'bra', 'BraA09t41933Z' => 'bra', 'C01p05210' => 'bna', 'C01p45690' => 'bna', 'C02p61330' => 'bna', 'C03p49480' => 'bna', 'C05p47100' => 'bna', 'C05p47110' => 'bna', 'C07p44790' => 'bna', 'C08p49990' => 'bna', 'C09p08050' => 'bna', 'C09p08060' => 'bna', 'CAN.G102.6' => 'can', 'CAN.G1228.29' => 'can', 'CAN.G1726.5' => 'can', 'CAN.G438.119' => 'can', 'CANSAT25G3169' => 'cansat', 'CANSAT54G1254' => 'cansat', 'CANSAT56G3272' => 'cansat', 'CANSAT80G1114' => 'cansat', 'CANSAT80G2151' => 'cansat', 'CARHR008340' => 'chi', 'CARHR093900' => 'chi', 'CARHR241550' => 'chi', 'CARHR274760' => 'chi', 'CARHR274770' => 'chi', 'Carub.0001s0781' => 'cru', 'Carub.0003s1831' => 'cru', 'Carub.0007s0700' => 'cru', 'Carub.0008s2174' => 'cru', 'Carub.0008s2175' => 'cru', 'Carub.0008s2176' => 'cru', 'Ca_02540_v3' => 'car', 'Ca_16360_v3' => 'car', 'Ca_17631_v3' => 'car', 'Ca_21779_v3' => 'car', 'CBR_g20016' => 'cbr', 'CBR_g34011' => 'cbr', 'Cc00_g07600' => 'ccan', 'Cc01_g08510' => 'ccan', 'Cc04_g07470' => 'ccan', 'Cc07_g18770' => 'ccan', 'CDE02G0998' => 'cde', 'CDE02G1247' => 'cde', 'CDE02G2613' => 'cde', 'CDE02G3243' => 'cde', 'CDE02G4064' => 'cde', 'CDE08G1660' => 'cde', 'Cfa009938' => 'cfa', 'Cfa019326' => 'cfa', 'Cfa019809' => 'cfa', 'Cfa022198' => 'cfa', 'Ciclev10001184m.g' => 'ccl', 'Ciclev10019240m.g' => 'ccl', 'Ciclev10019370m.g' => 'ccl', 'Ciclev10028632m.g' => 'ccl', 'CiPaw.03G120300' => 'cil', 'CiPaw.11G052800' => 'cil', 'CiPaw.14G094600' => 'cil', 'CiPaw.15G127300' => 'cil', 'ClCG01G011570' => 'cla', 'ClCG01G015340' => 'cla', 'ClCG03G012480' => 'cla', 'ClCG06G015680' => 'cla', 'COL.COLO4_06864' => 'col', 'COL.COLO4_10188' => 'col', 'COL.COLO4_22724' => 'col', 'COL.COLO4_35764' => 'col', 'Cpa.g.c36738' => 'cpa', 'Cpa.g.sc13.45' => 'cpa', 'Cpa.g.sc140.1' => 'cpa', 'Cpa.g.sc140.11' => 'cpa', 'Cpa.g.sc140.13' => 'cpa', 'Cpa.g.sc42.168' => 'cpa', 'Cpa.g.sc67.15' => 'cpa', 'Cpa.g.sc67.16' => 'cpa', 'Cpa.g.sc754.5' => 'cpa', 'Cpa.g.sc94.49' => 'cpa', 'Cpa.g.sc94.50' => 'cpa', 'Cpa.g.sc99.2' => 'cpa', 'Cpa.g.sc99.3' => 'cpa', 'Cre02.g116950' => 'cre', 'Cre03.g160000' => 'cre', 'Cre03.g162050' => 'cre', 'Cre06.g290400' => 'cre', 'Cre11.g467706' => 'cre', 'Cre11.g467785' => 'cre', 'Cre11.g469600' => 'cre', 'Cre11.g477800' => 'cre', 'CsaV3_1G002870' => 'csa', 'CsaV3_1G015200' => 'csa', 'CsaV3_1G043530' => 'csa', 'CsaV3_6G041560' => 'csa', 'CsaV3_UNG232240' => 'csa', 'CSS0009786' => 'camsi', 'CSS0018152' => 'camsi', 'CSS0027606' => 'camsi', 'CSS0034667' => 'camsi', 'CSS0040168' => 'camsi', 'CSS0049177' => 'camsi', 'DCAR_001205' => 'dca', 'DCAR_011558' => 'dca', 'DCAR_018202' => 'dca', 'DCAR_023185' => 'dca', 'Dinv08143' => 'din', 'Dinv17408' => 'din', 'Dinv24384' => 'din', 'Dinv40429' => 'din', 'Duzib068G1187' => 'dzi', 'Duzib170G0708' => 'dzi', 'Duzib205G1271' => 'dzi', 'Duzib205G1512' => 'dzi', 'Duzib264G0077' => 'dzi', 'Duzib264G1089' => 'dzi', 'ECA232G0502' => 'eca', 'ECA232G3750' => 'eca', 'ECA232G4339' => 'eca', 'ECA232G4674' => 'eca', 'ECA238G2405' => 'eca', 'ECA247G0276' => 'eca', 'EL10Ac5g11123' => 'bvu', 'EL10Ac5g11255' => 'bvu', 'EL10Ac6g15291' => 'bvu', 'EL10Ac7g16307' => 'bvu', 'Eucgr.B00702' => 'egr', 'Eucgr.B01265' => 'egr', 'Eucgr.J00560' => 'egr', 'Eucgr.J01293' => 'egr', 'Eucgr.K02528' => 'egr', 'Eucgr.K02530' => 'egr', 'Eucgr.L02060' => 'egr', 'Eucgr.L02064' => 'egr', 'FAN04G2323' => 'fan', 'FAN08G0910' => 'fan', 'FAN08G3403' => 'fan', 'FAN13G0112' => 'fan', 'FAN13G1473' => 'fan', 'FAN18G2590' => 'fan', 'FAN18G3650' => 'fan', 'FAN18G3757' => 'fan', 'FAN19G0829' => 'fan', 'FAN19G0875' => 'fan', 'FAN21G1240' => 'fan', 'FAN25G2103' => 'fan', 'FAN26G1915' => 'fan', 'FAN28G2289' => 'fan', 'FvH4_1g24510' => 'fve', 'FvH4_3g26560' => 'fve', 'FvH4_3g26570' => 'fve', 'FvH4_5g12660' => 'fve', 'FvH4_5g13910' => 'fve', 'Glyma.05G012850' => 'gma', 'Glyma.05G021400' => 'gma', 'Glyma.05G192600' => 'gma', 'Glyma.12G188200' => 'gma', 'Glyma.17G078000' => 'gma', 'Glyma.17G120900' => 'gma', 'Gohir.A03G069900' => 'ghi', 'Gohir.A05G383400' => 'ghi', 'Gohir.A12G265600' => 'ghi', 'Gohir.A13G221801' => 'ghi', 'Gohir.D03G096500' => 'ghi', 'Gohir.D04G031900' => 'ghi', 'Gohir.D12G265800' => 'ghi', 'Gohir.D12G265866' => 'ghi', 'Gohir.D13G225800' => 'ghi', 'Gorai.003G101100' => 'gra', 'Gorai.008G285500' => 'gra', 'Gorai.012G036200' => 'gra', 'Gorai.013G256700' => 'gra', 'GSVIVG01007870001' => 'vvi', 'GSVIVG01008242001' => 'vvi', 'GSVIVG01011230001' => 'vvi', 'GSVIVG01026467001' => 'vvi', 'GSVIVG01026793001' => 'vvi', 'GSVIVG01036156001' => 'vvi', 'HanXRQChr02g0059831' => 'han', 'HanXRQChr03g0070471' => 'han', 'HanXRQChr09g0251781' => 'han', 'HanXRQChr09g0269881' => 'han', 'HanXRQChr10g0295221' => 'han', 'HanXRQChr10g0300651' => 'han', 'HanXRQChr14g0433381' => 'han', 'HanXRQChr16g0502421' => 'han', 'HanXRQChr17g0543361' => 'han', 'Haze_07717' => 'cav', 'Haze_18621' => 'cav', 'Haze_21914' => 'cav', 'Haze_23305' => 'cav', 'Haze_25261' => 'cav', 'Haze_26937' => 'cav', 'Hma1.2p1_0060F.1_g033160' => 'hma', 'Hma1.2p1_0340F.1_g129850' => 'hma', 'Hma1.2p1_0568F.1_g180150' => 'hma', 'Hma1.2p1_0568F.1_g180160' => 'hma', 'Hma1.2p1_1113F.1_g258680' => 'hma', 'HPP92_000061' => 'vpl', 'HPP92_005669' => 'vpl', 'HPP92_006052' => 'vpl', 'HPP92_013948' => 'vpl', 'Hund02590' => 'sun', 'Hund18794' => 'sun', 'Lalb_Chr07g0178611' => 'lal', 'Lalb_Chr12g0197171' => 'lal', 'Lalb_Chr13g0302311' => 'lal', 'Lalb_Chr14g0375981' => 'lal', 'Lalb_Chr14g0375991' => 'lal', 'Lalb_Chr16g0392561' => 'lal', 'Lj1g0009434' => 'lja', 'Lj2A978G21' => 'lonja', 'Lj3g0014602' => 'lja', 'Lj3g0024965' => 'lja', 'Lj4C835T2' => 'lonja', 'Lj4g0005909' => 'lja', 'Lj4g0008764' => 'lja', 'Lj4g0011583' => 'lja', 'Lj4g0023799' => 'lja', 'Lj5A145G38' => 'lonja', 'Lj5C103T5' => 'lonja', 'Lsat_1_v5_gn_0_6440' => 'lsa', 'Lsat_1_v5_gn_1_63480' => 'lsa', 'Lsat_1_v5_gn_2_35600' => 'lsa', 'Lsat_1_v5_gn_2_37440' => 'lsa', 'Lsat_1_v5_gn_3_141121' => 'lsa', 'Lsat_1_v5_gn_4_111000' => 'lsa', 'Lsat_1_v5_gn_4_114000' => 'lsa', 'Lsat_1_v5_gn_4_115781' => 'lsa', 'Lsat_1_v5_gn_5_34720' => 'lsa', 'Lsat_1_v5_gn_7_76320' => 'lsa', 'Lsat_1_v5_gn_8_79781' => 'lsa', 'Lsat_1_v5_gn_9_115261' => 'lsa', 'Manes.01G020400' => 'mes', 'Manes.01G159100' => 'mes', 'Manes.06G085100' => 'mes', 'Manes.12G156900' => 'mes', 'Mapoly0001s0348' => 'mpo', 'Mapoly0023s0094' => 'mpo', 'Mapoly0029s0117' => 'mpo', 'Mapoly0049s0028' => 'mpo', 'Mapoly0214s0003' => 'mpo', 'MBI03_g20845_MAGBIO' => 'mbi', 'MBI05_g05626_MAGBIO' => 'mbi', 'MBI13_g29986_MAGBIO' => 'mbi', 'MBI17_g28776_MAGBIO' => 'mbi', 'MCO05G524' => 'mco', 'MCO07G211' => 'mco', 'MCO07G471' => 'mco', 'MCO10G368' => 'mco', 'MCO11G834' => 'mco', 'MD01G1005700' => 'mdo', 'MD03G1154900' => 'mdo', 'MD06G1202300' => 'mdo', 'MD06G1211800' => 'mdo', 'MD14G1211400' => 'mdo', 'MD14G1222300' => 'mdo', 'Medtr2g087270' => 'mtr', 'Medtr4g109500' => 'mtr', 'Medtr4g111985' => 'mtr', 'Medtr8g093800' => 'mtr', 'MELO3C008064.2' => 'cme', 'MELO3C015103.2' => 'cme', 'MELO3C017221.2' => 'cme', 'MELO3C025575.2' => 'cme', 'MELO3C035135.2' => 'cme', 'Migut.D01491' => 'egut', 'Migut.D01492' => 'egut', 'Migut.D01588' => 'egut', 'Migut.D01589' => 'egut', 'Migut.D01738' => 'egut', 'Migut.D01741' => 'egut', 'Migut.D01742' => 'egut', 'Migut.D01743' => 'egut', 'Migut.H00692' => 'egut', 'Migut.I00311' => 'egut', 'Migut.N02457' => 'egut', 'MSTRG.17683' => 'ama', 'MSTRG.22987' => 'ama', 'MSTRG.9271' => 'ama', 'Nitab4.5_0000380g0080' => 'nta', 'Nitab4.5_0000410g0030' => 'nta', 'Nitab4.5_0000504g0020' => 'nta', 'Nitab4.5_0001485g0180' => 'nta', 'Nitab4.5_0001491g0080' => 'nta', 'Nitab4.5_0001599g0120' => 'nta', 'Nitab4.5_0003575g0030' => 'nta', 'Nitab4.5_0003660g0060' => 'nta', 'Nitab4.5_0012564g0010' => 'nta', 'Nn2g14308' => 'nnu', 'Nn3g17442' => 'nnu', 'Nn3g20653' => 'nnu', 'Nn4g23728' => 'nnu', 'Nn5g28508' => 'nnu', 'Nn5g28522' => 'nnu', 'Oeu029215.1' => 'oeu', 'Oeu031813.2' => 'oeu', 'Oeu058292.1' => 'oeu', 'Os05g0440250' => 'osa', 'Os05g0440300' => 'osa', 'Os05g0440632' => 'osa', 'Os07g0164100' => 'osa', 'Os07g0602200' => 'osa', 'Os12g0182700' => 'osa', 'Peaxi162Scf00015g00729' => 'pax', 'Peaxi162Scf00098g00013' => 'pax', 'Peaxi162Scf00119g00930' => 'pax', 'Peaxi162Scf00119g00944' => 'pax', 'Peaxi162Scf00201g00236' => 'pax', 'PGR044G1429' => 'pgr', 'PGR083G1355' => 'pgr', 'PGR102G3106' => 'pgr', 'PGR119G1703' => 'pgr', 'PGSC0003DMG400005706' => 'stu', 'PGSC0003DMG400005895' => 'stu', 'PGSC0003DMG400024639' => 'stu', 'PGSC0003DMG401005535' => 'stu', 'Phvul.002G273200' => 'pvu', 'Phvul.003G176700' => 'pvu', 'Phvul.003G185200' => 'pvu', 'Phvul.005G120200' => 'pvu', 'Potri.004G092900' => 'ptr', 'Potri.005G064200' => 'ptr', 'Potri.009G020500' => 'ptr', 'Potri.012G060400' => 'ptr', 'Pp3c10_16170' => 'ppa', 'Pp3c13_17860' => 'ppa', 'Pp3c14_21020' => 'ppa', 'Pp3c21_17500' => 'ppa', 'Pp3c3_19120' => 'ppa', 'PRCOL_00001278' => 'pco', 'PRCOL_00001547' => 'pco', 'PRCOL_00003202' => 'pco', 'PRCOL_00005198' => 'pco', 'PRCOL_00006234' => 'pco', 'Prupe.2G016900' => 'ppe', 'Prupe.4G272300' => 'ppe', 'Prupe.5G204500' => 'ppe', 'Prupe.5G217800' => 'ppe', 'Prupe.6G143900' => 'ppe', 'Psat0s3618g0040' => 'psa', 'Psat2g014760' => 'psa', 'Psat3g118840' => 'psa', 'Psat4g043200' => 'psa', 'Psat5g203880' => 'psa', 'Psat5g260600' => 'psa', 'Psat6g202280' => 'psa', 'Psat7g045760' => 'psa', 'PSO017G1932' => 'pso', 'PSO017G2770' => 'pso', 'PSO017G2978' => 'pso', 'PSO017G5497' => 'pso', 'PSO017G7272' => 'pso', 'PSO063G1915' => 'pso', 'PSO170G2800' => 'pso', 'PSO339G0152' => 'pso', 'PSO384G0168' => 'pso', 'PSO478G0818' => 'pso', 'PSO478G1521' => 'pso', 'PSO478G4502' => 'pso', 'QL01p020087' => 'qlo', 'QL10p019416' => 'qlo', 'QL10p022503' => 'qlo', 'QL10p043125' => 'qlo', 'QL10p043184' => 'qlo', 'QL10p043267' => 'qlo', 'QL10p043286' => 'qlo', 'QL10p043345' => 'qlo', 'RcHm_v2.0_Chr1g0346631' => 'rch', 'RcHm_v2.0_Chr2g0121851' => 'rch', 'RcHm_v2.0_Chr5g0048241' => 'rch', 'RcHm_v2.0_Chr6g0252021' => 'rch', 'RcHm_v2.0_Chr6g0304611' => 'rch', 'RcHm_v2.0_Chr7g0183031' => 'rch', 'RcHm_v2.0_Chr7g0184671' => 'rch', 'Rhsim01G0201400' => 'rsi', 'Rhsim08G0136600' => 'rsi', 'Rhsim08G0146300' => 'rsi', 'Rhsim10G0133100' => 'rsi', 'Sabra04G0062400' => 'sbr', 'Sabra05G0053500' => 'sbr', 'Sabra09G0011800' => 'sbr', 'Sabra12G0043500' => 'sbr', 'SalBow1G2034' => 'sbo', 'SalBow1G6805' => 'sbo', 'SalBow1G7771' => 'sbo', 'SalBow5G2451' => 'sbo', 'SalBow5G2522' => 'sbo', 'Sc03g0005030' => 'sci', 'Sc03g0005040' => 'sci', 'Sc04g0004320' => 'sci', 'Sc10g0009540' => 'sci', 'Sc19g0005860' => 'sci', 'Sc21g0006820' => 'sci', 'Sed0000594' => 'sed', 'Sed0003489' => 'sed', 'Sed0006061' => 'sed', 'Sed0008132' => 'sed', 'Sed0017478' => 'sed', 'SEGI_09415' => 'sgi', 'SEGI_12166' => 'sgi', 'SEGI_15820' => 'sgi', 'SEGI_24328' => 'sgi', 'SEGI_25913' => 'sgi', 'SGA_v2.0_scaffold171G38938' => 'sas', 'SGA_v2.0_scaffold268G46226' => 'sas', 'SGA_v2.0_scaffold370G50105' => 'sas', 'SMO118G0445' => 'smo', 'SMO203G0267' => 'smo', 'SMO232G0082' => 'smo', 'SMO241G0020' => 'smo', 'SMO241G0029' => 'smo', 'SMO356G0044' => 'smo', 'Solyc01g009120.3' => 'sly', 'Solyc03g115150.4' => 'sly', 'Solyc03g119730.3' => 'sly', 'Solyc06g074080.3' => 'sly', 'Sopen01g004600' => 'spe', 'Sopen03g034210' => 'spe', 'Sopen03g038580' => 'spe', 'Sopen06g030500' => 'spe', 'Sp1g07100' => 'spa', 'Sp2g24350' => 'spa', 'Sp2g24360' => 'spa', 'Sp3g16610' => 'spa', 'Sp7g31180' => 'spa', 'TAR622G0805' => 'tar', 'TAR623G0033' => 'tar', 'TAR628G1683' => 'tar', 'TAR629G1683' => 'tar', 'TAR629G3345' => 'tar', 'THA.LOC104800509' => 'tha', 'THA.LOC104801191' => 'tha', 'THA.LOC104819490' => 'tha', 'THA.LOC104820404' => 'tha', 'Thecc.01G134400' => 'tca', 'Thecc.03G028900' => 'tca', 'Thecc.03G101100' => 'tca', 'Thecc.09G273600' => 'tca', 'Thhalv10003787m.g' => 'esa', 'Thhalv10007924m.g' => 'esa', 'Thhalv10020421m.g' => 'esa', 'Thhalv10025266m.g' => 'esa', 'TPR.G10982' => 'tpr', 'TPR.G2048' => 'tpr', 'TPR.G26787' => 'tpr', 'TPR.G36228' => 'tpr', 'TPR.G37345' => 'tpr', 'TPR.G4207' => 'tpr', 'TWI75G1875' => 'twi', 'TWI79G0588' => 'twi', 'TWI79G0844' => 'twi', 'TWI81G0178' => 'twi', 'TWI81G0708' => 'twi', 'unitig_26.g9658' => 'ugi', 'unitig_27.g25027' => 'ugi', 'unitig_46.g18490' => 'ugi', 'unitig_899.g14678' => 'ugi', 'vmacro12791' => 'vma', 'vmacro14322' => 'vma', 'vmacro17607' => 'vma', 'vmacro17672' => 'vma', 'VMungo0251G0496' => 'vmu', 'VMungo0540G2035' => 'vmu', 'VMungo1080G1022' => 'vmu', 'VMungo1215G0855' => 'vmu', 'VMungo1215G0938' => 'vmu', 'VMungo1215G1713' => 'vmu', 'VMungo1215G2334' => 'vmu', 'Zm00001eb108570' => 'zma', 'Zm00001eb148900' => 'zma', 'Zm00001eb300710' => 'zma', 'Zm00001eb348390' => 'zma', 'Zm00001eb348460' => 'zma' ) $gf_id = 'HOM05D001053' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001053' ) $data_identifier = 'HOM05D001053' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 13, 'cre' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 8, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 6, 'han' => (int) 9, 'cav' => (int) 6, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 4, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 11, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 5, 'ppe' => (int) 5, 'psa' => (int) 8, 'pso' => (int) 12, 'qlo' => (int) 8, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb348460' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1